##########################################
## 总目录
##########################################

export dna_preprocess_scripts=~/dna_preprocess_scripts
export config_path=${work_dir}/config

##########################################
## 软件
##########################################

export tools_path=~/tools/StandTools/
export gatk4=${tools_path}/gatk-4.1.7.0/gatk
export funcotator_ref=${tools_path}/gatk-4.1.7.0/funcotator_dataSources.v1.6.20190124s
export mosdepth=${tools_path}/mosdepth
export samtools=${tools_path}/samtools-1.2/samtools
export Rscript=${tools_path}/Rscript
export datamash=${tools_path}/datamash
export bedtools=${tools_path}/bedtools
export bcftools=${tools_path}/bcftools
export bgzip=${tools_path}/bgzip
export tabix=${tools_path}/tabix

##########################################
## 参考文件
##########################################

export ref=~/ref
export ref_path=~/ref
export seq_ref=${ref}/seq
export target_bed=${config_path}/Targets_region.bed
export ref_fasta=${ref}/seq/GRCh37.fa

##########################################
## 输出目录
##########################################

export vcf_path=${work_dir}/results/vcf
export qc_path=${work_dir}/results/Qc
export tmp_path=${work_dir}/results/tmp
export maf_path=${work_dir}/results/maf
export log_path=${work_dir}/results/log
export bam_path=${work_dir}/results/bam
export Tree_path=${work_dir}/results/tree
export Qsub_log_path=${work_dir}/results/Qsub_log
export facets_path=${work_dir}/results/Facets
export MSI_path=${work_dir}/results/msi
#export gvcf_path=${work_dir}/results/gvcf
#export plink_path=${work_dir}/results/plink
export vcf_qc_path=${work_dir}/results/vcf_qc
#export ibd_path=${plink_path}/ibd

mkdir -p ${maf_path}
mkdir -p ${Qsub_log_path}
mkdir -p ${Tree_path}
mkdir -p ${MSI_path}
#mkdir -p ${plink_path}
mkdir -p ${vcf_qc_path}
#mkdir -p ${ibd_path}

